[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [ccp4bb]: High and low B-factors
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Hello!
Sorry, there was a mistake. The mass is not 8000 kDa but 8000 Da.
Sorry for that.
RALF
On Thu, 28 Nov 2002, Ralf Bienert wrote:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> Hello!
>
> I have ESI as well as MALDI-TOF mass spectra showing one peak (~8000 kD)
> at the excepted mass for the Se-Met protein. So, I thought this is the evidence
> for 100 % Se-Met incorporation. I also produced the protein in a
> Met-auxotrophic strain.
>
> Ralf
>
>
> On Thu, 28 Nov 2002, Marko Hyvonen wrote:
>
> >
> > Are you sure you have 100 % Se-Met incorporation ? I would guess that if
> > part of your seleniums are in fact sulfurs, modelling the as seleniums
> > only would cause exactly what you describe now.
> >
> > Marko
> >
> >
> >
> > On Thu, 28 Nov 2002, Ralf Bienert wrote:
> >
> > > *** For details on how to be removed from this list visit the ***
> > > *** CCP4 home page http://www.ccp4.ac.uk ***
> > >
> > > Hello everybody!
> > >
> > > I solved a SAD structure to 1.8 A of a Se-Met protein and refine it with
> > > refmac5.
> > > However, I observed negative difference density around my Se-sites,
> > > together with high B-factors of this atoms. I think this is due to
> > > radiation damage. So far it is interpretable.
> > > But why do I have so low B-values for my CE atoms, even lower than the
> > > B-value of the other atoms of Se-Met.
> > > My question now is how to interprete this observation and how to deal with
> > > it. I just set the occupancy of both atoms to lower (same) values to get
> > > rid of the negative difference density, but is this the right way???? Of
> > > course, the B-value decresed, as well of CE.
> > >
> > > To get an idea I list my "worst" data (occupancy=1, B-value):
> > >
> > > N MSE 1.00 45.98 N
> > > CA MSE 1.00 45.15 C
> > > CB MSE 1.00 43.74 C
> > > CG MSE 1.00 44.29 C
> > > SE MSE 1.00 49.38 SE
> > > CE MSE 1.00 9.79 C
> > > C MSE 1.00 43.49 C
> > > O MSE 1.00 44.28 O
> > >
> > > N MSE 1.00 25.08 N
> > > CA MSE 1.00 25.90 C
> > > CB MSE 1.00 25.00 C
> > > CG MSE 1.00 29.97 C
> > > SE MSE 1.00 35.56 SE
> > > CE MSE 1.00 19.57 C
> > > C MSE 1.00 24.97 C
> > > O MSE 1.00 23.98 O
> > >
> > > Thanks in advance.
> > > Ralf
> > >
> > >
> > > *********************
> > > Ralf Bienert
> > > Crystallography Group
> > > MDC-Berlin
> > > *********************
> > >
> > >
> >
> >
> > ____________________________________
> >
> > Marko Hyvonen, PhD
> > Department of Biochemistry
> > University of Cambridge
> > http://www-cryst.bioc.cam.ac.uk/~marko
> > tel: +44-(0)1223-766 031 / 766 027
> > _______________________________________
> >
>